On Wed, 2014-09-17 at 14:39 -0300, George Tzotzos wrote:
> I’m using MMPBSA.py.MPI to calculate binding energies. The script I’m
> using is:
>
> Input file for running PB and GB
> &general
>
> interval=2, endframe=10000, verbose=1,
> # entropy=1,
> /
> &gb
> igb=1, saltcon=0.100
> /
> &pb
> inp=1, istrng=0.100,
> /
>
> Using inp=1 throws out warning messages indicating that inp=1 is the
> old default
I think the warnings are actually stating that the defaults for _other_
parameters in the &pb namelist are applicable to the inp=2 model, and
that they are being changed to the defaults for the inp=1 model that you
chose. So this is fine.
>
> Running the same calculation with inp=2 and comparing the results the
> discrepancies for the Poisson Bolzmann binding energies are pretty
> huge
This has been reported a number of times on this list. If inp=2 is
giving you physically unrealistic results, inp=1 may be the better model
to use for your system -- this has been discussed quite a bit on the
Amber list in the past.
>
> GENERALIZED BORN (inp=1) -22.3955 kcal/mol -22.7632 kcal/mol (Complex
> - Receptor - Ligand)
>
> POISSON BOLTZMANN (inp=1) -18.7747 kcal/mol 0.8206 kcal/mol (Complex
> - Receptor - Ligand)
inp=1 is PB only. The GB nonpolar model is basically only like inp=1 (a
simple SASA-based method that is purely unfavorable). I'm not quite
sure what the numbers you posted are supposed to mean. I'm guessing the
first is inp=1 and the second inp=2? If so, I'm surprised the GB
energies changed at all, and the PB energies certainly indicate a
difference in the nonpolar binding free energies. Neither is probably a
great choice for absolute binding affinities, but hopefully relative
binding affinities show far less dependence on the nonpolar model you
choose.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 17 2014 - 11:00:03 PDT
